Added a method to generate non-standard InChIs

bioclipse · Aug 16, 2012 · 3f033f3 · 3f033f3
1 parent 44def77
commit 3f033f3
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diff --git a/...i.business.test/src/net/bioclipse/inchi/business/test/AbstractInChIManagerPluginTest.java b/...i.business.test/src/net/bioclipse/inchi/business/test/AbstractInChIManagerPluginTest.java
@@ -39,6 +39,15 @@ public void testGenerate() throws Exception {
         Assert.assertEquals("InChI=1S/CH4/h1H4", inchiObj.getValue());
     }
 
+    @Test
+    public void testGenerateWithOptions() throws Exception {
+        IMolecule mol = cdk.fromSMILES("OC=O");
+        Assert.assertNotNull("Input structure is unexpectedly null", mol);
+        InChI inchiObj = inchi.generate(mol, "FixedH");
+        Assert.assertNotNull(inchiObj);
+        Assert.assertEquals("InChI=1/CH2O2/c2-1-3/h1H,(H,2,3)/f/h2H", inchiObj.getValue());
+    }
+
     @Test
     public void testGenerateNoStereo() throws Exception {
         IMolecule mol = cdk.fromSMILES("ClC(Br)(F)(O)");

diff --git a/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/IInChIManager.java b/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/IInChIManager.java
@@ -10,6 +10,8 @@
  ******************************************************************************/
 package net.bioclipse.inchi.business;
 
+import java.util.List;
+
 import net.bioclipse.core.PublishedClass;
 import net.bioclipse.core.PublishedMethod;
 import net.bioclipse.core.Recorded;
@@ -38,6 +40,17 @@ public interface IInChIManager extends IBioclipseManager {
     public BioclipseJob<InChI> generate(IMolecule molecule,
             BioclipseJobUpdateHook<InChI> h );
 
+    @Recorded
+    @PublishedMethod(
+        params = "IMolecule molecule, String options",
+        methodSummary = "Generates the InChI and InChIKey for the " +
+        		"given molecule, using the given options. This options String consists of " +
+        		"one or more, space-delimited options, such as FixedH.")
+    @TestMethods("testGenerateWithOptions")
+    public InChI generate(IMolecule molecule, String options) throws Exception;
+    public BioclipseJob<InChI> generate(IMolecule molecule, String options,
+            BioclipseJobUpdateHook<InChI> h );
+
     @Recorded
     @PublishedMethod(
         methodSummary = "Loads the InChI library.")

diff --git a/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/InChIManager.java b/plugins/net.bioclipse.inchi/src/net/bioclipse/inchi/business/InChIManager.java
@@ -87,6 +87,50 @@ public void generate( IMolecule molecule,
         }
     }
 
+    public void generate( IMolecule molecule, String options,
+            IReturner<InChI> returner,
+            IProgressMonitor monitor) 
+    throws Exception {
+    	monitor.beginTask("Calculating InChI", IProgressMonitor.UNKNOWN);
+    	// return early if InChI library could not be loaded
+    	if (!isAvailable()) {
+    		returner.completeReturn(InChI.FAILED_TO_CALCULATE);
+    		return;
+    	}
+
+    	Object adapted = molecule.getAdapter(IAtomContainer.class);
+    	if (adapted != null) {
+    		IAtomContainer container = (IAtomContainer)adapted;
+    		IAtomContainer clone = (IAtomContainer)container.clone();
+    		// remove aromaticity flags
+    		for (IAtom atom : clone.atoms())
+    			atom.setFlag(CDKConstants.ISAROMATIC, false);
+    		for (IBond bond : clone.bonds())
+    			bond.setFlag(CDKConstants.ISAROMATIC, false);
+    		InChIGenerator gen = factory.getInChIGenerator(clone, options);
+    		INCHI_RET status = gen.getReturnStatus();
+    		if(monitor.isCanceled())
+    			throw new OperationCanceledException();
+    		if (status == INCHI_RET.OKAY ||
+    				status == INCHI_RET.WARNING) {
+    			monitor.done();
+    			InChI inchi = new InChI();
+    			inchi.setValue(gen.getInchi());
+    			inchi.setKey(gen.getInchiKey());
+    			returner.completeReturn( inchi );
+    		} else {
+    			throw new InvalidParameterException(
+    					"Error while generating InChI (" + status + "): " +
+    							gen.getMessage()
+    					);
+    		}
+    	} else {
+    		throw new InvalidParameterException(
+    				"Given molecule must be a CDKMolecule"
+    				);
+    	}
+    }
+
     public String load() {
         if (factory == null) {
             try {